Microstructures of calcium silicate hydrates (C-S-H) are relevant to the mechanical properties and durability of cement-based materials. Random growth of the microstructures of C-S-H largely compromises the mechanical properties and durability. This paper proposes to utilize cellulose nanocrystals (CNCs) to modify the microstructures of C-S-H. This research investigates the effect of CNCs on the morphological, microstructural, and mechanical properties of C-S-H through dynamic light scattering (DLS), transmission electron microscopy (TEM), scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), thermogravimetry analysis (TGA), atomic force microscopy (AFM), and three-point bending tests. The results showed that CNCs effectively mitigated the agglomeration of C-S-H and generated C-S-H/CNC nanocomposites with highly ordered, layered, and dense microstructures. The C-S-H and CNCs in the C-S-H/CNC nanocomposites had strong interactions through hydrogen bonds and calcium ion coordination bonds. The strong interactions and ordered microstructures enable C-S-H/CNCs nanocomposites to achieve high strength and flexibility.